Single-cell landscape of long and short glandular trichomes in Nicotiana tabacum leaves

Summary Glandular trichomes (GTs) play a crucial role in plant defenses and the synthesis of secondary metabolites. Understanding the developmental trajectory of GTs is essential for unraveling their functional significance and potential applications. Here we established a comprehensive single-cell atlas of Nicotiana tabacum leaves, a model plant for GT studies. The atlas included a total of 40,433 cells and successfully captured both long GTs (LGTs) and short GTs (SGTs) from Nicotiana leaves. The developmental trajectories of these trichomes were delineated, revealing potential disparities in epidermal development. Comparative analysis of Arabidopsis and Nicotiana trichome development indicated limited similarity between Arabidopsis epidermal non-glandular trichomes and Nicotiana LGTs and SGTs, implying the essentiality of studying the genes directly involved in the development of Nicotiana GTs for a proper and comprehensive understanding of GT biology. Overall, our results provide profound insights into the developmental intricacies of the specialized GTs.


Supplemental Materials
Table S13 The highly expressed genes that are specifically common between the Arabidopsis epidermal trichome and tobacco long and short glandular trichome, related to STAR Methods.

Figure S1 .
Figure S1.Violin plots displaying the detected feature number (nFeature_RNA) and the read counts (nCount_RNA) in each sample, related to Figure 1.

Figure S2 .
Figure S2.The violin plot illustrates the distribution of gene expression in mitochondria (percent.mt)and chloroplasts (percent.ch)across all samples, related to Figure 1.

Figure
Figure S3.UMAP plots of the 6 samples from 3 Nicotiana accessions, demonstrating both the robust reproducibility between the two samples of the same accessions and the consistency in the number of cell types identified across different accessions, related to Figure 1.

Figure S4 .
Figure S4.Expression patterns of marker genes for cell types are displayed, related to Figure 1.(A) A dot plot illustrates the expression of leaf cell type marker genes across cell clusters.(B) A dot plot shows the expression of leaf cell type marker genes within various cell groups.

Figure S6 .
Figure S6.The distribution of various cell types among different accessions and samples is examined, related to Figure 1.(A) Bar chart illustrating the proportions of cell types among different accessions and samples.(B) Bar chart illustrating the numbers of different cell types among various accessions and samples.

Figure S7 .
Figure S7.Expression of tomato trichome marker genes in tobacco leaves, related to Figure 1.

Figure S8 .
Figure S8.The functional enrichment results of GT-specific expression genes are presented, related to Figure 1.(A) A network diagram displays LGT-specifically enriched GO terms.(B) A network diagram displays SGT-specifically enriched GO terms.

Figure S9 .
Figure S9.Expression profiles of the top three GT-specific genes in UMAP clusters, with in situ hybridization results on the right, related to Figure 1.(A) Display the specifically expressed genes identified in LGT.(B) Display the specifically expressed genes identified in SGT.

Figure S10 .
Figure S10.In situ hybridization images of tobacco glandular trichome marker genes, where 'negative' denotes negative controls and 'positive' represents positive results.'LGT' corresponds to Long Glandular Trichome, and 'SGT' refers to Short Glandular Trichome, related to Figure 1.

Figure S11 .
Figure S11.Genes specifically expressed in trichomes of different tobacco accessions, related to Figure 4. (A) Volcano plot displaying LGTs genes specifically expressed in different N. tabacum accessions.(B) Volcano plot displaying SGTs genes specifically expressed in different N. tabacum accessions.

Figure S12 .
Figure S12.The heatmap affirms that the trichome-specific genes identified from single-cell data in Arabidopsis are also highly expressed in the corresponding microarray transcriptomic data, related to Figure 5.

Figure S13 .
Figure S13.Specifically expressed genes in different cell types and their Gene Ontology (GO) enrichment results, related to Figure 5. (A)Heat map showing the identified cell type-specific differentially expressed genes, with the representative enriched functional terms displayed on the right.The bar chart in the middle illustrates the number of enriched genes.(B) Circular plot depicting the relationship between the shared specific genes in epidermal trichomes of Arabidopsis, LGTs and SGTs of N. tabacum, along with the associated GO terms.

Figure S14 .
Figure S14.GO enrichment analysis of genes specifically expressed in long and short glandular trichomes of tobacco, related to Figure 5. (A) Circular plot depicting the relationship between the shared specific genes in epidermal trichomes of Arabidopsis and LGTs of N. tabacum, along with the corresponding GO terms.(B) Circular plot depicting the relationship between the shared specific genes in epidermal trichomes of Arabidopsis and SGTs of N. tabacum, along with the corresponding GO terms.